As it happens: current directions in experimental evolution

Recent decades have seen a significant rise in studies in which evolution is observed and analysed directly—as it happens—under replicated, controlled conditions. Such ‘experimental evolution’ approaches offer a degree of resolution of evolutionary processes and their underlying genetics that is difficult or even impossible to achieve in more traditional comparative and retrospective analyses. In principle, experimental populations can be monitored for phenotypic and genetic changes with any desired level of replication and measurement precision, facilitating progress on fundamental and previously unresolved questions in evolutionary biology. Here, we summarize 10 invited papers in which experimental evolution is making significant progress on a variety of fundamental questions. We conclude by briefly considering future directions in this very active field of research, emphasizing the importance of quantitative tests of theories and the emerging role of genome-wide re-sequencing.

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Population genomics of parallel phenotypic evolution in stickleback across stream–lake ecological transitions

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2011.1552 ◽

2011 ◽

Vol 279 (1732) ◽

pp. 1277-1286 ◽

Cited By ~ 95

Author(s):

Bruce E. Deagle ◽

Felicity C. Jones ◽

Yingguang F. Chan ◽

Devin M. Absher ◽

David M. Kingsley ◽

...

Keyword(s):

Evolutionary Biology ◽

Population Genomics ◽

Haida Gwaii ◽

Single Nucleotide ◽

Genome Scans ◽

Genetic Changes ◽

Genome Wide ◽

Outlier Loci ◽

Genomic Regions

Understanding the genetics of adaptation is a central focus in evolutionary biology. Here, we use a population genomics approach to examine striking parallel morphological divergences of parapatric stream–lake ecotypes of threespine stickleback fish in three watersheds on the Haida Gwaii archipelago, western Canada. Genome-wide variation at greater than 1000 single nucleotide polymorphism loci indicate separate origin of giant lake and small-bodied stream fish within each watershed (mean F ST between watersheds = 0.244 and within = 0.114). Genome scans within watersheds identified a total of 21 genomic regions that are highly differentiated between ecotypes and are probably subject to directional selection. Most outliers were watershed-specific, but genomic regions undergoing parallel genetic changes in multiple watersheds were also identified. Interestingly, several of the stream–lake outlier regions match those previously identified in marine–freshwater and benthic–limnetic genome scans, indicating reuse of the same genetic loci in different adaptive scenarios. We also identified multiple new outlier loci, which may contribute to unique aspects of differentiation in stream–lake environments. Overall, our data emphasize the important role of ecological boundaries in driving both local and broadly occurring parallel genetic changes during adaptation.

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The Cardamine hirsuta genome offers insight into the evolution of morphological diversity

Nature Plants ◽

10.1038/nplants.2016.167 ◽

2016 ◽

Vol 2 (11) ◽

Cited By ~ 46

Author(s):

Xiangchao Gan ◽

Angela Hay ◽

Michiel Kwantes ◽

Georg Haberer ◽

Asis Hallab ◽

...

Keyword(s):

Evolutionary Biology ◽

Human Genetics ◽

Morphological Evolution ◽

Morphological Diversity ◽

Close Relative ◽

Gene Duplications ◽

Tandem Gene Duplication ◽

Genome Wide ◽

Differential Gene

Abstract Finding causal relationships between genotypic and phenotypic variation is a key focus of evolutionary biology, human genetics and plant breeding. To identify genome-wide patterns underlying trait diversity, we assembled a high-quality reference genome of Cardamine hirsuta, a close relative of the model plant Arabidopsis thaliana. We combined comparative genome and transcriptome analyses with the experimental tools available in C. hirsuta to investigate gene function and phenotypic diversification. Our findings highlight the prevalent role of transcription factors and tandem gene duplications in morphological evolution. We identified a specific role for the transcriptional regulators PLETHORA5/7 in shaping leaf diversity and link tandem gene duplication with differential gene expression in the explosive seed pod of C. hirsuta. Our work highlights the value of comparative approaches in genetically tractable species to understand the genetic basis for evolutionary change.

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Tell Me Where You’ve Been and I’ll Tell You How You’ll Evolve

mBio ◽

10.1128/mbio.02043-20 ◽

2020 ◽

Vol 11 (5) ◽

Author(s):

Marco Fumasoni

Keyword(s):

High Temperatures ◽

Adaptive Evolution ◽

Experimental Evolution ◽

Evolutionary Biology ◽

Genetic Basis ◽

Microbial Populations ◽

Evolutionary Processes ◽

Link Type ◽

Selection Experiments ◽

Evolutionary Trajectories

ABSTRACT The reproducibility of adaptive evolution is a long-standing debate in evolutionary biology. Kempher et al. (M. L. Kempher, X. Tao, R. Song, B. Wu, et al., mBio 11:e00569-20, 2020, https://doi.org/10.1128/mBio.00569-20) used experimental evolution to investigate the effect of previous evolutionary trajectories on the ability of microbial populations to adapt to high temperatures. Despite the divergence caused by adaptation to previous environments, all populations reproducibly converged on similar final levels of fitness. Nevertheless, the genetic basis of adaptation depended on past selection experiments, reinforcing the idea that previous adaptation can dictate the trajectories of later evolutionary processes.

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Genome-wide disruption of DNA methylation by 5-aza-2’-deoxycytidine in the parasitoid wasp Nasonia vitripennis

10.1101/437202 ◽

2018 ◽

Cited By ~ 1

Author(s):

Nicola Cook ◽

Darren J Parker ◽

Frances Turner ◽

Eran Tauber ◽

Bart A Pannebakker ◽

...

Keyword(s):

Dna Methylation ◽

Evolutionary Biology ◽

Sex Allocation ◽

Phenotypic Expression ◽

Parasitoid Wasp ◽

Nasonia Vitripennis ◽

Genomic Conflict ◽

Genome Wide ◽

A Genome

AbstractDNA methylation of cytosine residues across the genome influences how genes and phenotypes are regulated in a wide range of organisms. As such, understanding the role of DNA methylation and other epigenetic mechanisms has become very much a part of mapping genotype to phenotype, a major question in evolutionary biology. Ideally, we would like to manipulate DNA methylation patterns on a genome-wide scale, to help us to elucidate the role that epigenetic modifications play in phenotypic expression. Recently, the demethylating agent 5-aza-2’-deoxycytidine (5-aza-dC; commonly used in the epigenetic treatment of certain cancers), has been deployed to explore the epigenetic regulation of a number of traits of interest to evolutionary ecologists, including facultative sex allocation in the parasitoid wasp Nasonia vitripennis. In a recent study, we showed that treatment with 5-aza-dC did not ablate the facultative sex allocation response in Nasonia, but shifted the patterns of sex allocation in a way predicted by genomic conflict theory. This was the first (albeit indirect) experimental evidence for genomic conflict over sex allocation facilitated by DNA methylation. However, that work lacked direct evidence of the effects of 5-aza-dC on DNA methylation, and indeed the effect of the chemical has since been questioned in Nasonia. Here, using whole-genome bisulphite sequencing of more than 4 million CpGs, across more than 11,000 genes, we demonstrate unequivocally that 5-aza-dC disrupts methylation on a large scale across the Nasonia vitripennis genome. We show that the disruption can lead to both hypo- and hyper-methylation, may vary across tissues and time of sampling, and that the effects of 5-aza-dC are context- and sequence specific. We conclude that 5-aza-dC does indeed have the potential to be repurposed as a tool for studying the role of DNA methylation in evolutionary ecology, whilst many details of its action remain to be discovered.Author SummaryShedding light on the mechanistic basis of phenotypes is a major aim in the field of evolutionary biology. If we understand how phenotypes are controlled at the molecular level, we can begin to understand how evolution has shaped that phenotype and conversely, how genetic architecture may constrain trait evolution. Epigenetic markers (such as DNA methylation) also influence phenotypic expression by regulating how and when genes are expressed. Recently, 5-aza-2’-deoxycytidine (5-aza-dC), a hypomethylating agent used in the treatment of certain cancers, has been used to explore the epigenetic regulation of traits of interest to evolutionary ecologists. Previously, we used 5-aza-dC to validate a role for DNA methylation in facultative sex allocation behaviour in the parasitoid wasp Nasonia vitripennis. However, the direct effects of the chemical were not examined at that point and its efficacy in insects was questioned. Here, we demonstrate that 5-aza-dC disrupts DNA methylation on a genome-wide scale in a context- and sequence-specific manner and results in both hypo- and hyper-methylation. Our work demonstrates that 5-aza-dC has the potential to be repurposed as a tool for studying the role of DNA methylation in phenotypic expression.

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Genome Wide Analysis Reveals the Role of VadA in Stress Response, Germination, and Sterigmatocystin Production in Aspergillus nidulans Conidia

Microorganisms ◽

10.3390/microorganisms8091319 ◽

2020 ◽

Vol 8 (9) ◽

pp. 1319 ◽

Cited By ~ 1

Author(s):

Ye-Eun Son ◽

Hee-Soo Park

Keyword(s):

Stress Response ◽

Secondary Metabolism ◽

Aspergillus Nidulans ◽

Gene Clusters ◽

Tube Formation ◽

Spore Viability ◽

Genetic Changes ◽

Genome Wide ◽

Trehalose Biosynthesis

In the Aspergillus species, conidia are asexual spores that are infectious particles responsible for propagation. Conidia contain various mycotoxins that can have detrimental effects in humans. Previous study demonstrated that VadA is required for fungal development and spore viability in the model fungus Aspergillus nidulans. In the present study, vadA transcriptomic analysis revealed that VadA affects the mRNA expression of a variety of genes in A. nidulans conidia. The genes that were primarily affected in conidia were associated with trehalose biosynthesis, cell-wall integrity, stress response, and secondary metabolism. Genetic changes caused by deletion of vadA were related to phenotypes of the vadA deletion mutant conidia. The deletion of vadA resulted in increased conidial sensitivity against ultraviolet stress and induced germ tube formation in the presence and absence of glucose. In addition, most genes in the secondary metabolism gene clusters of sterigmatocystin, asperfuranone, monodictyphenone, and asperthecin were upregulated in the mutant conidia with vadA deletion. The deletion of vadA led to an increase in the amount of sterigmatocystin in the conidia, suggesting that VadA is essential for the repression of sterigmatocystin production in conidia. These results suggest that VadA coordinates conidia maturation, stress response, and secondary metabolism in A. nidulans conidia.

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Epigenetic Alterations and an Increased Frequency of Micronuclei in Women with Fibromyalgia

Nursing Research and Practice ◽

10.1155/2013/795784 ◽

2013 ◽

Vol 2013 ◽

pp. 1-12 ◽

Cited By ~ 7

Author(s):

Victoria Menzies ◽

Debra E. Lyon ◽

Kellie J. Archer ◽

Qing Zhou ◽

Jenni Brumelle ◽

...

Keyword(s):

System Development ◽

Chronic Widespread Pain ◽

Nervous System Development ◽

Future Research ◽

Genetic Changes ◽

Workplace Productivity ◽

Genome Wide ◽

Methylation Patterns ◽

Healthcare Expenses

Fibromyalgia (FM), characterized by chronic widespread pain, fatigue, and cognitive/mood disturbances, leads to reduced workplace productivity and increased healthcare expenses. To determine if acquired epigenetic/genetic changes are associated with FM, we compared the frequency of spontaneously occurring micronuclei (MN) and genome-wide methylation patterns in women with FM (n=10) to those seen in comparably aged healthy controls (n=42(MN);n=8(methylation)). The mean (sd) MN frequency of women with FM (51.4 (21.9)) was significantly higher than that of controls (15.8 (8.5)) (χ2=45.552; df = 1;P=1.49×10-11). Significant differences (n=69sites) in methylation patterns were observed between cases and controls considering a 5% false discovery rate. The majority of differentially methylated (DM) sites (91%) were attributable to increased values in the women with FM. The DM sites included significant biological clusters involved in neuron differentiation/nervous system development, skeletal/organ system development, and chromatin compaction. Genes associated with DM sites whose function has particular relevance to FM included BDNF, NAT15, HDAC4, PRKCA, RTN1, and PRKG1. Results support the need for future research to further examine the potential role of epigenetic and acquired chromosomal alterations as a possible biological mechanism underlying FM.

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Roles of adenosine and cytosine methylation changes and genetic mutations in adaptation to different temperatures

10.1101/822080 ◽

2019 ◽

Cited By ~ 1

Author(s):

Matthieu Bruneaux ◽

Ilkka Kronholm ◽

Roghaieh Ashrafi ◽

Tarmo Ketola

Keyword(s):

Experimental Evolution ◽

Cytosine Methylation ◽

Regulation Of Gene Expression ◽

Phenotypic Traits ◽

Phenotypic Variance ◽

Epigenetic Changes ◽

Genetic Changes ◽

Different Temperatures ◽

The Relationship

AbstractEpigenetic modifications have been found to be involved in evolution, but the relative contributions of genetic and epigenetic variation in adaptation are unknown. Furthermore, previous studies on the role of epigenetic changes in adaptation have nearly exclusively focused on cytosine methylation in eukaryotes. We collected phenotypic, genetic, and epigenetic data from populations of the bacteriumSerratia marcescensthat had undergone experimental evolution in contrasting temperatures to investigate the relationship between environment, genetics, epigenetic, and phenotypic traits. The genomic distribution of methylated adenosines (m6A) pointed to their role in regulation of gene expression, while cytosine methylation (m4C) likely has a different role inS. marcescens. We found both environmentally induced and likely spontaneous methylation changes. There was very little indication that methylation changes were under genetic control. Decomposition of phenotypic variance suggested that both genetic and epigenetic changes contributed to phenotypic variance with slightly higher contribution from genetic changes. Overall, our results suggest that while genetic changes likely are responsible for the majority of adaptation, adenosine methylation changes have potential to contribute to adaptation as well.

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Allele frequency divergence reveals ubiquitous influence of positive selection in Drosophila

PLoS Genetics ◽

10.1371/journal.pgen.1009833 ◽

2021 ◽

Vol 17 (9) ◽

pp. e1009833

Author(s):

Jason Bertram

Keyword(s):

Allele Frequency ◽

Evolutionary Biology ◽

Polymorphic Locus ◽

Allele Frequencies ◽

Intermediate Allele ◽

Genome Wide ◽

Signature Of Selection ◽

Basic Objective ◽

Genomic Regions

Resolving the role of natural selection is a basic objective of evolutionary biology. It is generally difficult to detect the influence of selection because ubiquitous non-selective stochastic change in allele frequencies (genetic drift) degrades evidence of selection. As a result, selection scans typically only identify genomic regions that have undergone episodes of intense selection. Yet it seems likely such episodes are the exception; the norm is more likely to involve subtle, concurrent selective changes at a large number of loci. We develop a new theoretical approach that uncovers a previously undocumented genome-wide signature of selection in the collective divergence of allele frequencies over time. Applying our approach to temporally resolved allele frequency measurements from laboratory and wild Drosophila populations, we quantify the selective contribution to allele frequency divergence and find that selection has substantial effects on much of the genome. We further quantify the magnitude of the total selection coefficient (a measure of the combined effects of direct and linked selection) at a typical polymorphic locus, and find this to be large (of order 1%) even though most mutations are not directly under selection. We find that selective allele frequency divergence is substantially elevated at intermediate allele frequencies, which we argue is most parsimoniously explained by positive—not negative—selection. Thus, in these populations most mutations are far from evolving neutrally in the short term (tens of generations), including mutations with neutral fitness effects, and the result cannot be explained simply as an ongoing purging of deleterious mutations.

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On Future Directions in Pathology

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100053991 ◽

1982 ◽

Vol 40 ◽

pp. 274-277

Author(s):

Benjamin F. Trump ◽

Irene K. Berezesky ◽

Raymond T. Jones

Keyword(s):

Electron Microscopy ◽

Transmission Electron Microscopy ◽

Clinical Pathology ◽

Future Directions ◽

Diagnostic Pathology ◽

The Past ◽

Transmission Electron ◽

Organ Systems ◽

The Many

The role of electron microscopy and associated techniques is assured in diagnostic pathology. At the present time, most of the progress has been made on tissues examined by transmission electron microscopy (TEM) and correlated with light microscopy (LM) and by cytochemistry using both plastic and paraffin-embedded materials. As mentioned elsewhere in this symposium, this has revolutionized many fields of pathology including diagnostic, anatomic and clinical pathology. It began with the kidney; however, it has now been extended to most other organ systems and to tumor diagnosis in general. The results of the past few years tend to indicate the future directions and needs of this expanding field. Now, in addition to routine EM, pathologists have access to the many newly developed methods and instruments mentioned below which should aid considerably not only in diagnostic pathology but in investigative pathology as well.

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